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PDBsum entry 1vzw

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Isomerase PDB id
1vzw
Jmol
Contents
Protein chain
224 a.a. *
Ligands
SO4 ×2
GOL
Waters ×226
* Residue conservation analysis
PDB id:
1vzw
Name: Isomerase
Title: Crystal structure of the bifunctional protein pria
Structure: Phosphoribosyl isomerase a. Chain: a. Synonym: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino) methylideneamino] imidazole-4-carboxamide isomerase, phosphoribosylformimino-5-aminoimidazole carboxamide ribot isomerase, n-(5'-phosphoribosyl)anthranilate isomerase, pr engineered: yes
Source: Streptomyces coelicolor. Organism_taxid: 1902. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: neb impact cn.
Resolution:
1.80Å     R-factor:   0.164     R-free:   0.205
Authors: J.Kuper,M.Wilmanns
Key ref:
J.Kuper et al. (2005). Two-fold repeated (betaalpha)4 half-barrels may provide a molecular tool for dual substrate specificity. EMBO Rep, 6, 134-139. PubMed id: 15654319 DOI: 10.1038/sj.embor.7400330
Date:
27-May-04     Release date:   19-Jan-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P16250  (HIS4_STRCO) -  Phosphoribosyl isomerase A
Seq:
Struc:
240 a.a.
224 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.5.3.1.16  - 1-(5-phosphoribosyl)-5-
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Histidine Biosynthesis (early stages)
      Reaction: 1-(5-phospho-beta-D-ribosyl)-5-((5-phospho-beta-D- ribosylamino)methylideneamino)imidazole-4-carboxamide = 5-((5-phospho-1- deoxy-D-ribulos-1-ylamino)methylideneamino)-1-(5-phospho-beta-D- ribosyl)imidazole-4-carboxamide
   Enzyme class 3: E.C.5.3.1.24  - Phosphoribosylanthranilate isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1- deoxy-D-ribulose 5-phosphate
N-(5-phospho-beta-D-ribosyl)anthranilate
= 1-(2-carboxyphenylamino)-1- deoxy-D-ribulose 5-phosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   5 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1038/sj.embor.7400330 EMBO Rep 6:134-139 (2005)
PubMed id: 15654319  
 
 
Two-fold repeated (betaalpha)4 half-barrels may provide a molecular tool for dual substrate specificity.
J.Kuper, C.Doenges, M.Wilmanns.
 
  ABSTRACT  
 
Some bacterial genomes contain an incomplete set of genes encoding phosphoribosyl isomerases, raising the question of whether there exists broadened substrate specificity for the missing gene products. To investigate the underlying molecular principles of this hypothesis, we have determined the crystal structure of the bifunctional enzyme PriA from Streptomyces coelicolor at 1.8 A resolution. It consists of a (betaalpha)(8)-barrel fold that is assembled by two symmetric (betaalpha)(4) half-barrels. The structure shows how its active site may catalyse the isomerization reactions of two different substrates, and we provide a plausible model of how the smaller of the two substrates could be bound in two different orientations. Our findings expand the half-barrel ancestor concept by demonstrating that symmetry-related half-barrels could provide a smart solution to cope with dual substrate specificity. The data may help to unravel molecular rationales regarding how organisms with miniature genomes can keep central biological pathways functional.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 HisA and TrpF catalyse similar reactions in histidine and tryptophan biosynthesis. HisA and TrpF catalyse the isomerizations of the aminoaldoses ProFAR and PRA to the aminoketoses N'-((5'-phosphoribulosyl)formimino)-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) and 1-(o-carboxyphenylamino)-1-deoxyribulose 5-phosphate (CdRP). The PriA protein catalyses both reactions in Streptomyces coelicolor and Mycobacterium tuberculosis. These organisms lack a trpf gene.
Figure 4.
Figure 4 Active site of PriA. (A) Superimposition of the active sites of PriA (blue) and HisA (green). Active-site residues and the two bound sulphate ions are shown in stick mode. The carbon atoms are in the colour of the corresponding C[ ]trace. Oxygen molecules are coloured red and sulphur in yellow. (B) Superimposition of the active sites of PriA (blue) and TrpF (black). Active-site residues and the two bound sulphate ions are shown in stick mode using atom-type colours. (C) PriA active sites with the HisA product analogue rPRFAR. The rPRFAR coordinates have been taken from the superimposed HisF structure (not shown) in the presence of rPRFAR (Chaudhuri et al, 2001). Residues most probably involved in catalysis are highlighted green, surrounded by red circles, in this panel and in all following panels with modelled complexes. (D) PriA active site with the TrpF product analogue rCdRP. The rCdRP coordinates were obtained from the superimposed TrpF structure in complex with rCdRP (Henn-Sax et al, 2002). (E) PriA active site with the TrpF product analogue rCdRP modelled binding to the second phosphate binding site. The rCdRP coordinates were obtained from the TrpF structure in complex with rCdRP (Henn-Sax et al, 2002) superimposed with the C-terminal half-barrel of PriA. Complete PriA was then superimposed using the coordinates obtained from the C-terminal half-barrel. (A -E) Prepared with DINO (http://www.dino3d.org) and rendered with POVRAY 3.6 (http://www.povray.org).
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO Rep (2005, 6, 134-139) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21321225 A.V.Due, J.Kuper, A.Geerlof, J.P.Kries, and M.Wilmanns (2011).
Bisubstrate specificity in histidine/tryptophan biosynthesis isomerase from Mycobacterium tuberculosis by active site metamorphosis.
  Proc Natl Acad Sci U S A, 108, 3554-3559.
PDB codes: 2y85 2y88 2y89
20525292 C.Kim, J.Basner, and B.Lee (2010).
Detecting internally symmetric protein structures.
  BMC Bioinformatics, 11, 303.  
  20066665 L.Noda-García, A.R.Camacho-Zarco, K.Verdel-Aranda, H.Wright, X.Soberón, V.Fülöp, and F.Barona-Gómez (2010).
Identification and analysis of residues contained on beta --> alpha loops of the dual-substrate (beta alpha)8 phosphoribosyl isomerase A specific for its phosphoribosyl anthranilate isomerase activity.
  Protein Sci, 19, 535-543.
PDB code: 2x30
20551137 P.Carbonell, and J.L.Faulon (2010).
Molecular signatures-based prediction of enzyme promiscuity.
  Bioinformatics, 26, 2012-2019.  
19237570 J.Claren, C.Malisi, B.Höcker, and R.Sterner (2009).
Establishing wild-type levels of catalytic activity on natural and artificial (beta alpha)8-barrel protein scaffolds.
  Proc Natl Acad Sci U S A, 106, 3704-3709.
PDB code: 2w79
17253090 J.Payandeh, and E.F.Pai (2007).
Enzyme-driven speciation: crystallizing Archaea via lipid capture.
  J Mol Evol, 64, 364-374.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.